Once-stout rush defense has been shredded in two straight games and may be hard-pressed to stop Rams Thursday night, especially if Willis is unable to play

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The Colts and running back Ahmad Bradshaw (No. 44) couldn't be stopped on the ground last week by the 49ers. (Photo by Thearon W. Henderson/Getty Images)

In their loss to the Colts Sunday, the 49ers gave up 179 yards rushing.

The stat is the clearest indication that this Niners defense isn’t what it has been over the past two seasons.

As Chase Stuart of the New York Times noted this week, the Jim Harbaugh-led 49ers had only given up 170 yards or more on the ground once in his first 38 games (including the postseason) as San Francisco’s head coach. The 49ers have now allowed more than 170 yards rushing in consecutive games.

Is it just a blip? Or is it a trend?

In 2012, the 49ers were fourth in the NFL, giving up just 94.2 yards on the ground per game, an average of 3.7 yards per carry. In 2011, they ranked No. 1, giving up just 77.2 yards per game and 3.5 per carry. This season they rank 28th, giving up 138 yards per game and 3.9 yards a try, including six touchdown runs -- just one less than they allowed in 16 games a year ago.

As the 49ers (1-2) head into their divisional game against the Rams (1-2) in St. Louis Thursday night, the defensive fall from grace by San Francisco is even more alarming than the team’s struggles on offense.

Oddsmakers have made the 49ers 3-point favorites, but if the 49ers can’t plug the holes in their run defense, it’s possible the Rams could put them in a 1-3 hole that might be too deep to climb out of in an NFC West that features the undefeated Seahawks.

Vic Fangio, the 49ers defensive coordinator, admits his unit hasn’t done a good job against the run, but also says the stats are a bit misleading.

“I think it’s been we’ve let a couple of them (runs) pop, which we haven’t done in the past, which skews the statistics,” he told the Bay Area media Tuesday. “And we’ve been in games where they’ve been able to hand it off a high amount of times (because of leads). So, I think it’s a combination that we haven’t been as sharp and the type of games we’ve been in.”

So far, the Rams have been a pass-first team, rushing for only 171 yards in three games. Darryl Richardson has been the lead ballcarrier, with 98 yards on 30 attempts. Quarterback Sam Bradford is averaging 47 passes per game, but some of that relates to the Rams playing from behind. In two games against the 49ers last season, the Rams were able to run the ball effectively with the now-departed Steven Jackson in the first game (a tie), but didn’t have much success in the second game (a Rams win).

Fangio still sees the Rams as a running team, despite the numbers.

“I do believe that the Rams will try and run the ball,” Fangio said. “That to me is their roots.”

If Willis – who was unable to practice Tuesday because of an injured groin – is out of the lineup Thursday, Michael Whilhoite will take his place. That’s a big target for the Rams. Willis, since he came into the league, has been terrific against the run. Dan Skuta and rookie Corey Lemonier, meanwhile, will be plugged into Smith’s spot at right outside linebacker. Already, the 49ers are missing starting nose tackle Ian Williams, who’s been replaced by Glenn Dorsey.

So what will it take for the 49ers to stop the Rams running game Thursday? Fangio says every defender needs to play his role over the entire game. The 49ers need to play smart. There can be no breakdowns.

“The last two weeks … we were in low-scoring defensive battles and we were the first defense to crack,” he said of the losses to Seattle and Indianapolis. “And we were ultimately the second-best defense on the field in those two games.”

Thursday night, the 49ers' run defense surely will be tested again. Rams coach Jeff Fisher is intent on getting his run game going, and the Niners will have to prove to him that they can stop Richardson and backup Isaiah Pead.

“We’ve got to hand it off more,” Fisher told reporters this week. “We haven’t had the opportunities – we’ve gotten behind. We’ve got to get back to that early in the game.”